// Converts an array of strings to an array of float32.
func StringArrayAsFloat32Array(v []string) []float32 {
data := make([]float32, len(v))
for i := 0; i < len(v); i++ {
x := strings.TrimSpace(v[i])
data[i] = what.Atof32(x)
}
return data
}
// Load an inpcrd file into this system
func (mol *System) LoadRst(inpcrdFilename string) {
inpcrdFile, err := os.Open(inpcrdFilename)
if err != nil {
fmt.Println("Error opening inpcrd:", err)
return
}
// defer == awesome!
defer inpcrdFile.Close()
inpcrd := bufio.NewReader(inpcrdFile)
// Header line - discard
s, err := inpcrd.ReadString('\n')
// Number of atoms
s, err = inpcrd.ReadString('\n')
n, _ := strconv.Atoi(strings.TrimSpace(s))
numCoords := mol.NumAtoms() * 3
if n*3 != numCoords {
fmt.Fprintf(os.Stderr, "Inpcrd says it has %d atoms but I'm expecting %d instead.\n", n, numCoords)
return
}
// Now we know how many tokens to expect. They are all of length 12,
// with up to 6 per line.
mol.Coords = make(map[int][]float32)
frame := 0
mol.Coords[frame] = make([]float32, numCoords)
numThings := 6
thingLen := 12
ctr := 0
for err == nil {
s, err = inpcrd.ReadString('\n')
// s contains some number of things
n := (len(s) - 1) / thingLen
if n > numThings {
n = numThings
}
thisFrame := mol.Coords[frame]
for i := 0; i < n*thingLen && ctr < numCoords; i += thingLen {
thisFrame[ctr] = what.Atof32(s[i : i+thingLen])
ctr++
}
}
// TODO: if it has a box, read the box, and move on to the next frame
if mol.GetInt("POINTERS", IFBOX) > 0 {
fmt.Fprintf(os.Stderr, "There's a box! We should do something about this.\n")
}
}
// Assumes file pointer is at the start of a frame
func GetNextFrameFromTrajectory(trj *bufio.Reader, numAtoms int, hasBox bool) ([]float32, error) {
// Calculate how many lines per frame
linesPerFrame := numAtoms * 3 / 10
if numAtoms*3%10 != 0 {
linesPerFrame++
}
// fmt.Println("Lines per frame:", linesPerFrame);
// var ok bool
var coords = make([]float32, numAtoms*3)
coords = <-coordsFreeList
// if (!ok) {
// fmt.Println("Allocating a new coords buffer.")
// coords = make([]float32, numAtoms*3)
// }
//
ci := 0
for i := 0; i < linesPerFrame; i++ {
// Read and trim a line
line, err := trj.ReadString('\n')
if err != nil {
return nil, err
}
line = trimSpace(line)
// Each token is ended by whitespace or eol.
for b := 0; b < len(line); {
var e int
// Advance to end of token
for e = b; e < len(line) && line[e] != ' ' && line[e] != '\n' && line[e] != '\t'; e++ {
}
//fmt.Println(b, e, line[b:e]);
coords[ci] = what.Atof32(line[b:e])
ci++
// Now, e is either at end of line or points to whitespace.
// Advance b to start of next token or eol
for b = e; b < len(line) && (line[b] == ' ' || line[b] == '\n' || line[b] == '\t'); b++ {
}
}
}
// Eat box line
if hasBox {
trj.ReadString('\n')
}
return coords, nil
}
// Loads an AMBER system - both a prmtop and inpcrd.
func LoadSystem(prmtopFilename string) *System {
var mol System
mol.Blocks = make(map[string][]string)
mol.Formats = make(map[string][]string)
prmtopFile, err := os.Open(prmtopFilename)
if err != nil {
fmt.Println("Error opening prmtop:", err)
return nil
}
// defer == awesome!
defer prmtopFile.Close()
prmtop := bufio.NewReader(prmtopFile)
// Set up us the regular expression
formatRe, _ := regexp.Compile("[(]([0-9]+)([aIE]+)([0-9.]+)[)]")
// Eat header line
s, err := prmtop.ReadString('\n')
//fmt.Println(s);
// Get first FLAG line
s, err = prmtop.ReadString('\n')
for err == nil {
//fmt.Println(s);
if len(s) < 5 {
break
}
blockName := strings.TrimSpace(s[6 : len(s)-1])
mol.Blocks[blockName] = make([]string, 0)
// FORMAT line
s, err = prmtop.ReadString('\n')
fmtSpec := formatRe.FindStringSubmatch(s)
var numThings, thingLen int
if len(fmtSpec) == 4 {
numThings, _ = strconv.Atoi(fmtSpec[1])
//thingType = fmtSpec[2];
lenSpec := what.Atof32(fmtSpec[3])
thingLen = int(lenSpec)
mol.Formats[blockName] = fmtSpec
} else {
fmt.Println("Couldn't understand format specifier - bad prmtop")
fmt.Println(fmtSpec, s)
return nil
}
// Now that we know what type of data to expect, read it
// until we hit another FLAG line
for err == nil {
s, err = prmtop.ReadString('\n')
if len(s) >= 5 && s[0:5] == "%FLAG" {
break
}
// s contains some number of things
n := (len(s) - 1) / thingLen
if n > numThings {
n = numThings
}
for i := 0; i < (n * thingLen); i += thingLen {
mol.Blocks[blockName] = append(mol.Blocks[blockName], s[i:i+thingLen])
}
}
}
return &mol
}